huelsenbeck12-13notes - Lectures 12 13 Wednesday April 1...

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Lectures 12 & 13 Wednesday, April 1, 2009 & Friday, April 3, 2009 Phylogenetic tree (phylogeny) Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system is hierarchical. Species in the same genus had a common ancestor more recently than species in different genera. The only figure in the Origin illustrated his idea. He introduced the idea of a phylogenetic tree . A phylogenetic tree represents the history of most groups of species: For a phylogenetic tree to be a good description of the history of a group, the time it takes for new species to form (represented by the splitting of lineages) has to be very short compared to how long each species was present. The phylogeny of humans, chimps, gorillas and bonobos is typical and thought to be roughly accurate . A few groups of plants, such as those in the genus Clarkia , do not have a tree-like history because many species are allopolyploids. The history of Clarkia and other such groups is reticulate (net-like) in which some species have two ancestors. Information in a phylogenetic tree: The pattern of branching indicates ancestry. The branch lengths indicate times. Cladogram: A cladogram summarizes the branching pattern but contains no information about times. Be sure to understand the difference between a phylogenetic tree and a cladogram. A phylogenetic tree represents the pattern of evolution: A tree is a convenient summary of what actually happened. If you could replay the webcast of life, you could discover the tree that describes the true history of a group of species. Phylogenetic trees and classification Darwin and taxonomy: Darwin did not address the practical problem of how to use evolutionary history to classify species into higher groups. The problem was then and is still that, although there is a phylogenetic tree that describes the history of most groups, the correct tree is usually not known. With the advent of DNA sequencing, much effort is going into inferring the phylogenies of all major groups. The Tree of Life project ( is an international effort to join phylogenetic trees of different groups into a single tree that describes the overall pattern of evolution. Terminology: A monophyletic group is one that contains an ancestral species and all of its descendants. Mammals are a monophyletic group. A monophyletic group is often called a clade. A paraphyletic group is one that contains an ancestral species and some but not all of its descendants. The family Pongidae
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(orangutans, chimpanzees, bonobos and gorillas) is paraphyletic. It does not include modern and extinct humans which are descended from a pongid ancestor. Phylogenetic systematics:
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huelsenbeck12-13notes - Lectures 12 13 Wednesday April 1...

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